KATANA - a charge-sensitive triggering system for the Sπ\piRIT experiment

KATANA - the Krakow Array for Triggering with Amplitude discrimiNAtion - has been built and used as a trigger and veto detector for the S$\pi$RIT TPC at RIKEN. Its construction allows operating in magnetic field and providing fast response for ionizing particles, giving the approximate forward multiplicity and charge information. Depending on this information, trigger and veto signals are generated. The article presents performance of the detector and details of its construction. A simple phenomenological parametrization of the number of emitted scintillation photons in plastic scintillator is proposed. The effect of the light output deterioration in the plastic scintillator due to the in-beam irradiation is discussed.Comment: 14 pages, 11 figure

Parameterizing neural networks for disease classification

Neural networks are one option to implement decision support systems for health care applications. In this paper, we identify optimal settings of neural networks for medical diagnoses: The study involves the application of supervised machine learning using an artificial neural network to distinguish between gout and leukaemia patients. With the objective to improve the base accuracy (calculated from the initial set-up of the neural network model), several enhancements are analysed, such as the use of hyperbolic tangent activation function instead of the sigmoid function, the use of two hidden layers instead of one, and transforming the measurements with linear regression to obtain a smoothened data set. Another setting we study is the impact on the accuracy when using a data set of reduced size but with higher data quality. We also discuss the tradeoff between accuracy and runtime efficiency

Pilot study on developing a decision support tool for guiding re-administration of chemotherapeutic agent after a serious adverse drug reaction

<p>Abstract</p> <p>Background</p> <p>Currently, there are no standard guidelines for recommending re-administration of a chemotherapeutic drug to a patient after a serious adverse drug reaction (ADR) incident. The decision on whether to rechallenge the patient is based on the experience of the clinician and is highly subjective. Thus the aim of this study is to develop a decision support tool to assist clinicians in this decision making process.</p> <p>Methods</p> <p>The inclusion criteria for patients in this study are: (1) had chemotherapy at National Cancer Centre Singapore between 2004 to 2009, (2) suffered from serious ADRs, and (3) were rechallenged. A total of 46 patients fulfilled the inclusion criteria. A genetic algorithm attribute selection method was used to identify clinical predictors for patients' rechallenge status. A Naïve Bayes model was then developed using 35 patients and externally validated using 11 patients.</p> <p>Results</p> <p>Eight patient attributes (age, chemotherapeutic drug, albumin level, red blood cell level, platelet level, abnormal white blood cell level, abnormal alkaline phosphatase level and abnormal alanine aminotransferase level) were identified as clinical predictors for rechallenge status of patients. The Naïve Bayes model had an AUC of 0.767 and was found to be useful for assisting clinical decision making after clinicians had identified a group of patients for rechallenge. A platform independent version and an online version of the model is available to facilitate independent validation of the model.</p> <p>Conclusion</p> <p>Due to the limited size of the validation set, a more extensive validation of the model is necessary before it can be adopted for routine clinical use. Once validated, the model can be used to assist clinicians in deciding whether to rechallenge patients by determining if their initial assessment of rechallenge status of patients is accurate.</p

The ASY-EOS experiment at GSI: investigating the symmetry energy at supra-saturation densities

The elliptic-flow ratio of neutrons with respect to protons in reactions of neutron rich heavy-ions systems at intermediate energies has been proposed as an observable sensitive to the strength of the symmetry term in the nuclear Equation Of State (EOS) at supra-saturation densities. The recent results obtained from the existing FOPI/LAND data for $^{197}$Au+$^{197}$Au collisions at 400 MeV/nucleon in comparison with the UrQMD model allowed a first estimate of the symmetry term of the EOS but suffer from a considerable statistical uncertainty. In order to obtain an improved data set for Au+Au collisions and to extend the study to other systems, a new experiment was carried out at the GSI laboratory by the ASY-EOS collaboration in May 2011.Comment: Talk given by P. Russotto at the 11th International Conference on Nucleus-Nucleus Collisions (NN2012), San Antonio, Texas, USA, May 27-June 1, 2012. To appear in the NN2012 Proceedings in Journal of Physics: Conference Series (JPCS

DNA damage signalling prevents deleterious telomere addition at DNA breaks

The response to DNA damage involves regulation of multiple essential processes to maximize the accuracy of DNA damage repair and cell survival 1. Telomerase has the potential to interfere with repair by inappropriately adding telomeres to DNA breaks. It was unknown whether cells modulate telomerase in response to DNA damage, to increase the accuracy of repair. Here we report that telomerase action is regulated as a part of the cellular response to a DNA double-strand break (DSB). Using yeast, we show that the major ATR/Mec1 DNA damage signalling pathway regulates telomerase action at DSBs. Upon DNA damage, MEC1-RAD53-DUN1-dependent phosphorylation of the telomerase inhibitor Pif1 occurs. Utilizing a separation of function PIF1 mutation, we show that this phosphorylation is required for the Pif1-mediated telomerase inhibition that takes place specifically at DNA breaks, but not telomeres. Hence DNA damage signalling down-modulates telomerase action at a DNA break via Pif1 phosphorylation, thus preventing aberrant healing of broken DNA ends by telomerase. These findings uncover a novel regulatory mechanism that coordinates competing DNA end-processing activities and thereby promotes DNA repair accuracy and genome integrity

Circular DNA Intermediate in the Duplication of Nile Tilapia vasa Genes

vasa is a highly conserved RNA helicase involved in animal germ cell development. Among vertebrate species, it is typically present as a single copy per genome. Here we report the isolation and sequencing of BAC clones for Nile tilapia vasa genes. Contrary to a previous report that Nile tilapia have a single copy of the vasa gene, we find evidence for at least three vasa gene loci. The vasa gene locus was duplicated from the original site and integrated into two distant novel sites. For one of these insertions we find evidence that the duplication was mediated by a circular DNA intermediate. This mechanism of gene duplication may explain the origin of isolated gene duplicates during the evolution of fish genomes. These data provide a foundation for studying the role of multiple vasa genes in the development of tilapia gonads, and will contribute to investigations of the molecular mechanisms of sex determination and evolution in cichlid fishes

Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes

Wittler R, Chauve C. Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. BMC Bioinformatics. 2011;12(Suppl. 9):S21

Isoscaling in central Sn+Sn collisions at 270 MeV/u

Experimental information on fragment emissions is important in understanding the dynamics of nuclear collisions and in the development of transport model simulating heavy-ion collisions. The composition of complex fragments emitted in the heavy-ion collisions can be explained by statistical models, which assume that thermal equilibrium is achieved at collision energies below 100 MeV/u. Our new experimental data together with theoretical analyses for light particles from Sn+Sn collisions at 270 MeV/u, suggest that the hypothesis of thermal equilibrium breaks down for particles emitted with high transfer momentum. To inspect the system's properties in such limit, the scaling features of the yield ratios of particles from two systems, a neutron-rich system of ${}^{132}\mathrm{Sn}+{}^{124}\mathrm{Sn}$ and a nearly symmetric system of ${}^{108}\mathrm{Sn}+{}^{112}\mathrm{Sn}$, are examined in the framework of the statistical multifragmentation model and the antisymmetrized molecular dynamics model. The isoscaling from low energy particles agree with both models. However the observed breakdown of isoscaling for particles with high transverse momentum cannot be explained by the antisymmetrized molecular dynamics model